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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatctagatttatttagtatgcaactaatacatcatatttgttcagatagtcttgcctaatcgaattactgaatgggatgtgtcctacttttcagAACAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAG

Basic information

species Oryza sativa
transcript LOC_Os02g31290.2
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 2
gtgatctagatttatttagtatgcaactaata-catcatatttgttcagatagtcttgcctaatcgaattactgaatgggatgtgtcctacttttcagAACAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAG
            ||  | | ||  |||| ||| | |  |||| ||| |||    |||| ||  ||   ||||| |||| |||     || |||||||||| || || ||||| ||||||||||||||||| |||||||||||||||||||||||||| |||||||||
-----------gtagattgaatttaactcataaccttgtattagttgagacta-cttgtctgctcatgttactaaatgagat-caatctccttttcagAATAAATGTAATGTCGGCTATGCTTTCATCAACATGACCAATCCTCAGCATATCATTCCGTTTTATCAG

upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 12
--------gtgatctagatttatttagtatgcaactaatacatcatatttgttcagatagtcttgcctaatcgaattactgaatgggatgtgtcctacttttcagAACAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAG
            | |  |||||  |  || || ||     | |  |||| ||| |||     ||   |  ||   ||||| |||| |||     || |||||||||| || || ||||| ||||||||||||||||| ||||||||| ||||||||||||||||||||||||||
gtagtttgaaactttgaatttaactcataagcgaccggggccttgtattagttgagactacttt-tgtgttcatgttactaaatgagat-caatctccttttcagAATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCAGCATATCATTCCATTTTATCAG

upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 11
--------gtgatctagatttatttagtatgcaa--ctaatacatcatatttgttcagatagtcttgcctaatcg-aattactgaatgggatgt-gtcctact-tttcagAACAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAG
        | |  |||  ||| ||   || | ||  || ||  | || |   ||  || |  |  |   |      ||  |   |||   || |   |||    ||||||||||| |||||||| || ||||||||||||||| | |   | ||| |  | ||  | ||||||| | ||
gcaagcaggcgtcctaccttttttatataagaaagtcttattaagcagacacgtagaggttttggtattttgcaataacgatctaatctaatcttaccctgtcatttcagAACAAATGCAATGTGGGATATGCTTTCATCAATCTTATTGAACCTGAAAAGATTGTCCCATTTTTTAAG

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|58687890|gb|CK076577.1|CK076577
EST:     AAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG                         AACAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCAT
genomic: AAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAGgtgatctaga ... tacttttcagAACAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCAT
EST: gi|58691922|gb|CK080609.1|CK080609
EST:     AAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG                         AATAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCAT
genomic: AAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAGgtgatctaga ... tacttttcagAACAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCAT
EST: gi|58657140|gb|CK045820.1|CK045820
EST:     AAATCATAAAGGGACTTATGATTTTATTTACCTACGGAGTGGACTTCAAG                         AACAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCAT
genomic: AAATCATAAAGGGACTTATGATTTTATTTACCTAC-CAATTGACTTCAAGgtgatctaga ... tacttttcagAACAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCAT
EST: gi|56158059|gb|C72031.2|C72031
EST:     AAAATCATAAAGGGACTTATGATTTTNTTTACCTACCAATTGACTTCAAG                         AACAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCAT
genomic: AAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAGgtgatctaga ... tacttttcagAACAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCAT
EST: gi|66930475|gb|CX117323.1|CX117323
EST:     AAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAG                         AACAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCAT
genomic: AAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAGgtgatctaga ... tacttttcagAACAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCAT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 67 (upstream exon), 69 (downstream exon)
Score: 49

GTACACCTCAAAGATGCTTCTAGCTGCTATTGATGAAAATCATAAAGGGACTTATGATTTTATTTACCTACCAATTGACTTCAAGgtgatctaga ... tacttttcagAACAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcagatagtcttgcctaatcgaattactgaatgggatgtgtcctacttttcagAACAAGTGCAATGTAGGCTATGCTTTCATCAATATGACCAATCCTCAGCATATCATTCCATTTTATCAG
              gcctaat  putative branch site (score: 49)
                                          tcctacttttc  putative PPT
                       aattact  TA-rich tract